library(drake)
library(tidyverse)
loadd(model_data_with_na, model_data, imputed_data)
Look at NA values in raw data
map_int(model_data_with_na, ~sum(!is.na(.)))
## iso3c n_amr_events
## 190 59
## health_expend_perc migrant_pop_per_capita
## 183 190
## population ab_export_bin
## 190 162
## english_spoken human_consumption_ddd
## 190 68
## livestock_pcu ab_export_per_capita
## 164 87
## ab_import_per_capita livestock_consumption_kg_per_capita
## 161 31
## gdp_per_capita tourism_outbound_per_capita
## 190 44
## tourism_inbound_per_capita pubcrawl_per_capita
## 111 180
## promed_mentions_per_capita
## 189
model_data_with_na %>%
filter(pubcrawl_per_capita == 0 | is.na(pubcrawl_per_capita)) %>%
nrow()
## [1] 33
model_data_with_na %>%
filter(promed_mentions_per_capita == 0 | is.na( promed_mentions_per_capita)) %>%
nrow()
## [1] 1
model_data_with_na %>%
filter(ab_export_per_capita == 0 | is.na( ab_export_per_capita)) %>%
nrow()
## [1] 103
Look at NA values and distributions post-NA processing
map_int(model_data, ~sum(!is.na(.)))
## iso3c n_amr_events
## 190 190
## health_expend_perc ln_migrant_pop_per_capita
## 183 190
## ln_population ab_export_bin
## 190 162
## english_spoken human_consumption_ddd
## 190 68
## ln_livestock_pcu ln_ab_export_per_capita
## 164 190
## ln_ab_import_per_capita ln_livestock_consumption_kg_per_capita
## 161 31
## ln_gdp_per_capita ln_tourism_outbound_per_capita
## 190 44
## ln_tourism_inbound_per_capita ln_pubcrawl_per_capita
## 111 190
## ln_promed_mentions_per_capita
## 190
map_lgl(model_data, ~any(is.infinite(.))) # confirm no infinite values
## iso3c n_amr_events
## FALSE FALSE
## health_expend_perc ln_migrant_pop_per_capita
## FALSE FALSE
## ln_population ab_export_bin
## FALSE FALSE
## english_spoken human_consumption_ddd
## FALSE FALSE
## ln_livestock_pcu ln_ab_export_per_capita
## FALSE FALSE
## ln_ab_import_per_capita ln_livestock_consumption_kg_per_capita
## FALSE FALSE
## ln_gdp_per_capita ln_tourism_outbound_per_capita
## FALSE FALSE
## ln_tourism_inbound_per_capita ln_pubcrawl_per_capita
## FALSE FALSE
## ln_promed_mentions_per_capita
## FALSE
model_data %>%
select(-iso3c, -n_amr_events, -english_spoken) %>%
gather() %>%
ggplot(aes(x = value)) +
geom_histogram() +
facet_wrap(key~., scales = "free")
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 596 rows containing non-finite values (stat_bin).
model_data %>%
dplyr::select(-iso3c, -ln_livestock_pcu, -ln_ab_import_per_capita, -ab_export_bin, -english_spoken) %>%
PerformanceAnalytics::chart.Correlation(., histogram = TRUE, pch = 19, method = "spearman")
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
Look at imputed data
plot(imputed_data) # On convergence, the different streams should be freely intermingled with one another, without showing any definite trends. Convergence is diagnosed when the variance between different sequences is no larger than the variance within each individual sequence.
show_imputes(imputed_data, m = imputed_data[["m"]], raw = model_data)
## Note: Using an external vector in selections is ambiguous.
## ℹ Use `all_of(m)` instead of `m` to silence this message.
## ℹ See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
## This message is displayed once per session.
imp <- complete(imputed_data)
imp %>%
dplyr::select(-iso3c) %>%
PerformanceAnalytics::chart.Correlation(., histogram = TRUE, pch = 19, method = "spearman")
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties